I have set up a coral run with 6 domains and I want to correlate the movement of domains of 1 with 3 and 2 with 4. Everytime I came up with an error message "groupping is not compatible with initial configuration". In trying to find the problem with my input files I also tried fixing domains, but this yielded the error message "fixation is not compatible with initial configuration".

I spent a great deal of time trying to find my problem, but as soon as I moved back to the version of Coral in ATSAS 2.5.2-1 everything worked perfectly. Is there any reason for the difference in behaviour for the two versions?

It appears to be all due to the length of the linkers. The distance between the N- and C- termini of adjacent subunits must be greater than some specified maximum distance for linkers of a given length.

All domains came from positions in a crystal structure, and I removed sections of loop between subunits and called them linkers. These linkers ranged in length from 6-9 AA and this caused problems. When I arbitrarily changed the length of all linkers to 9 AA, everything worked fine. This is not ideal, but at least I understand why it wasn't working.